|
| Status |
Public on Feb 26, 2015 |
| Title |
IDC-Patient4 |
| Sample type |
SRA |
| |
|
| Source name |
Patient 4
|
| Organism |
Homo sapiens |
| Characteristics |
individual: Patient 4
sample type: DCIS-IDC tandem lesion
cell type: IDC cells
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was prepared using (All prep Qiagen Kit) according to the manufacturers protocol
Libraries were prepared according to illumina TruSeq RNA Sample Prep. (LT) Protocol
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2500 |
| |
|
| Description |
Sample name: IDC4
Invasive ductal carcinoma (IDC), biopsied from patient No.4
|
| Data processing |
Paired Fastq sequence files were imported to CLC Genomics Workbench (version 7.5)and mapped to the human reference genome (hg19)
Ensembl database (GRCh37.74.gtf) was used for gene annotation…
Total number of reads mapped to the gene is used as the total counts for the gene, and the values were transformed by adding 1 followed by log2 transformation.
Transformed data was quantile normalized before the analysis of differential gene expression between two groups (DCIS vs IDC).
Empirical analysis of differential gene expression was performed between two groups (DCIS vs IDC) using ‘Exact Test"
Genome_build: human reference genome (hg19)
Supplementary_files_format_and_content: Excel file of all genes and of BCL9 normalized values
|
| |
|
| Submission date |
Feb 25, 2015 |
| Last update date |
May 15, 2019 |
| Contact name |
Hanan Elsarraj |
| E-mail(s) |
helsarraj@kumc.edu
|
| Organization name |
University of Kansas Medical Center
|
| Department |
Pathology and Laboratory Medicine
|
| Lab |
Fariba Behbod
|
| Street address |
3901 Rainbow Blvd.
|
| City |
Kansas City |
| State/province |
KS |
| ZIP/Postal code |
66160 |
| Country |
USA |
| |
|
| Platform ID |
GPL16791 |
| Series (1) |
| GSE66301 |
Gene expression profiling of patient's DCIS-IDC tandem lesions by RNA sequencing analysis |
|
| Relations |
| BioSample |
SAMN03375256 |
| SRA |
SRX890422 |
